Healthy Carrot Muffins

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These healthy carrot muffins are made with whole wheat flour, maple syrup, cold-pressed rapeseed oil, and fresh carrots for a nutritious breakfast. Lightly spiced with pumpkin pie spice, these carrot muffins are also perfect for fall!

Carrot muffins in a 6-cup muffin tray in front of a bottle of Clark's Pure Maple Syrup.

If it wasn’t abundantly clear from my love letter to carrot cake back in April, you should know that I’m obsessed with adding carrots to my baked goods. Cakes, puddings, muffins, cupcakes, french toast, pancakes, you name it. Everything sweet tastes better with a little shredded carrot.

This time of year is particularly exciting because I get to combine my favourite spice mixture – pumpkin pie spice! – with all the fresh, in-season carrots. Haven’t tried this pairing yet? You’re in for a mind-blowing experience, my friend.

Whip out your muffin pans right now, and let’s bake these pumpkin pie spiced healthy carrot muffins together!

A male hand reaching for a naturally sweetened breakfast muffin out of a 6-cup muffin tray on a white board.

Are carrot muffins healthy?

In general, carrot muffins are not healthy, and anyone who has tried to convince you otherwise is a liar. Don’t let the allure of added fruit or vegetables deceive you. Bakery-style muffins contain an insane amount of saturated fats and refined sugars. As an example, one blueberry muffin from Starbucks contains a whopping 12 grams of fat and 29 grams of sugar!

The good news? I would argue these spiced carrot muffins do belong on the healthier end of the muffin spectrum. We’re using whole wheat flour for extra fibre and added nutrients and rapeseed oil instead of butter. Rapeseed oil contains the lowest saturated fat content of all the vegetable oils and is high in essential fatty acids and vitamin E.

The Greek yogurt keeps these muffins incredibly moist and adds a welcome punch of protein, probiotics, calcium, and potassium.

These healthy carrot muffins are also lightly naturally sweetened with maple syrup and sweet in-season carrots instead of refined sugar. They’re not overly sweet, which I prefer in a muffin, and are super flavourful thanks to the pumpkin pie spice!

Refined sugar free muffins sitting on a cooling rack with a bottle of pure maple syrup.

How to make pumpkin pie spice

A few weeks ago on my Instagram Stories, I showed you how to make pumpkin pie spice. Because it’s such an integral part of this recipe, I’m including it here, but you can also check out this video if you want to see it prepped in action.

You’ll need:

  • A clean jar with a lid
  • 3 tbsp ground cinnamon
  • 2 tsp ground ginger
  • 2 tsp ground nutmeg
  • 1 ½ tsp ground allspice
  • 1 ½ tsp ground cloves

To make the spice, add all of the ingredients to the jar, seal the lid, and shake until fully combined.

Pumpkin pie spice is my favourite spice to use during autumn. It reminds me so much of home, of falling coloured leaves, Thanksgiving dinners, and comforting fall baking. I love adding it to my smoothies, morning coffee, warm oatmeal, and even chili!

The spice is incredibly warming and lends a subtle heat to these healthy carrot muffins – a perfect pairing for the hearty root veg.

Healthy carrot muffin on a plate being drizzled with pure maple syrup from a vintage spoon.

Tips for making the best healthy carrot muffins

Make sure all of your dry ingredients are fresh. I made the mistake of testing this recipe three times before I realised that my whole wheat flour had gone rancid! Before you start baking, always ensure your dry ingredients haven’t been left in the cupboard for too long. This includes flour, ground spices, and any leavening agents.

You can test flour by smell – if it smells rancid, it is. Spices can usually be tested by taste; if they aren’t particularly pungent, grab some new ones. Test leavening agents by adding them to a boiling water and vinegar solution. Not fizzing? They’re dead.

Use full-fat yogurt. Low-fat or 0-fat varieties will usually have sugar added to them to make them taste reasonable. Check the back of the package. In general, the first 5 grams of sugar in a 100g serving are attributed to milk sugar (lactose); anything over that usually means sugar has been added to the product.

Use farm-fresh carrots. Carrots are in-season right now, making them wonderfully sweet and crunchy. Use the best produce you can afford and trust me, it’ll make a huge difference to these healthy carrot muffins.

Make sure your rapeseed oil is cold-pressed. Cold-pressed oils are unrefined; they haven’t been heated above 37ºC (100ºF), meaning the oil retains its nutrients, delicate flavour, and aroma. Cold-pressed also guarantees that no added chemicals, preservatives, or harmful solvent residues were added to the final product.

These healthy carrot muffins are lightly spiced with pumpkin pie spice, made with whole wheat flour, rapeseed oil, and naturally sweetened with maple syrup. The perfect cozy fall breakfast!

Looking for more refined sugar free breakfast recipes?

I love these healthy carrot muffins warmed up and topped with a little almond butter for breakfast on a crisp fall day.

If you make this recipe, let me know by snapping a picture and tagging me on Instagram @naturallysweet_kitchen. I love seeing your creations and sharing them in my Stories. Or let me know you love these muffins by leaving a comment and rating below!

Carrot muffins packed with fibre, vitamins, and protein and naturally sweetened with maple syrup.
5 from 2 votes

Healthy Carrot Muffins

These lightly spiced healthy carrot muffins are made with whole wheat flour, maple syrup, rapeseed oil, and fresh carrots for a nutritious breakfast.

Category Breakfast
Keyword carrot muffins, healthy carrot muffins, healthy muffins
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Serves 12
Author Amanda | Naturally Sweet Kitchen


  • 225 g whole wheat flour
  • 3 tsp pumpkin pie spice
  • 2 tsp baking powder
  • ½ tsp baking soda
  • 200 g Greek yogurt room temperature
  • 1 tsp pure vanilla extract
  • 180 ml pure maple syrup
  • 60 ml cold-pressed rapeseed oil
  • 1 large egg room temperature
  • 225 g shredded carrot


  1. Preheat the oven to 190ºC (375ºF) and grease a 12-cup muffin tin with non-stick spray.
  2. In a large bowl, whisk together the flour, pumpkin pie spice, baking powder, and baking soda. Set aside.
  3. Add the yogurt, vanilla, maple syrup, oil, and egg to another bowl and whisk well to combine.
  4. Make a well in the dry ingredients and pour the wet ingredients into it. Stir until just combined. Fold in the shredded carrot. Do not overmix.
  5. Fill the muffin tin cavities completely with the batter. Bake for 16-20 minutes, or until a toothpick inserted comes out clean.
  6. Allow the muffins to cool in the tin for 7 minutes, then remove them to a wire rack to finish cooling.


  • These muffins will keep sealed in an airtight container at room temperature for up to 3 days.
  • The muffins can be frozen in an airtight container for up to 3 months.

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  1. This is the best muffin I have tried. They are so tasty, moist and flavourful. They also keep so well in the freezer that I can make a batch and bring them out a few at a time. Great recipe. Thanks

  2. Just finished a batch of these muffins and they are so light, moist and tasty. Great recipe, thanks, breakfast on the go for the week.

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